The present paper reports the results of the application of the Smoothed Particle Hydrodynamics (SPH) method to model the wave run-up over an armour breakwater. The units that form the outer layer of the structure have been modelled in 3D to validate the response under wave attacks. The open-source GPU DualSPHysics code has been used because of its capability to simulate millions of particles required for an accurate modelling. The run-up heights have been computed and compared with empirical solutions. The results are in agreement with the ones obtained using literature formulae.